Pelagibacter ubique

Pelagibacter, with the single species P. ubique, was isolated in 2002 and given a specific name,^[1] although it has not yet been validly published according to the bacteria in the entire world. It can make up about 25% of all microbial plankton cells, and in the summer they may account for approximately half the cells present in temperate ocean surface water. The total abundance of P. ubique and relatives is estimated to be about 2 × 10²⁸ microbes.^[4]

It is rod or crescent shaped and one of the smallest self-replicating cells known, with a length of 0.37-0.89 carbon cycle.

Its discovery was the subject of "Oceans of Microbes", Episode 5 of "Intimate Strangers: Unseen Life on Earth" by PBS.^[7]

Cultivation

Several strains of Pelagibacter ubique have been cultured thanks to improved isolation techniques.^[8] The most studied strain is HTCC1062 (high-throughput cultivation collection).^[1]

The factors that regulate SAR11 populations are still largely unknown. They have sensors for nitrogen, phosphate, and iron limitation, and a very unusual requirement for reduced sulfur compounds.^[9] It is hypothesised that they have been molded by evolution in a low nutrient ecosystem, such as the Sargasso Sea where it was first discovered.^[10]

A population of P. ubique cells can double every 29 hours, which is fairly slow, but they can replicate under low nutrient conditions.^[11]

P. ubique can be grown on a defined, artificial medium with additions of reduced sulfur, glycine, pyruvate and vitamins.^[12]

Genome

The genome of P. ubique strain HTCC1062 was completely sequenced in 2005 showing that P. ubique has the smallest ^[26]

See also

• Prochlorococcus
• Synechococcus

References

1. ^ ^{a b c} Michael S. Rappé; Stephanie A. Connon; Kevin L. Vergin; Stephen J. Giovannoni (2002). "Cultivation of the ubiquitous SAR11 marine bacterioplankton clade".  
2. ^ List of Candidate species entry in  ]
3. ^ R. M. Morris, et al. (2002). "SAR11 clade dominates ocean surface bacterioplankton communities".  
4. ^ "Candidatus Pelagibacter Ubique." European Bioinformatics Institute. European Bioinformatics Institute, 2011. Web. 08 Jan. 2012. http://www.ebi.ac.uk/2can/genomes/bacteria/Candidatus_Pelagibacter_ubique.html
5. ^ ^{a b c d} Stephen J. Giovannoni, H. James Tripp, et al. (2005). "Genome Streamlining in a Cosmopolitan Oceanic Bacterium".  
6. ^ ^{a b c} [6], Gauthier, Nicholas; Zinman, Guy; D’Antonio, Matteo; Abraham, Michael. Comparative Microbial Genomics DTU course. 2005.
7. ^ View "Oceans of Microbes" http://www.podcastdirectory.com/podshows/4339749
8. ^ Stingl, U.; Tripp, H. J.; Giovannoni, S. J. (2007). "Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site". The ISME Journal 1 (4).  
9. ^ H. James Tripp; Joshua B. Kitner; Michael S. Schwalbach; John W. H. Dacey; et al. (April 2008). "SAR11 marine bacteria require exogenous reduced sulfur for growth". Nature 452 (7188): 741–4.  
10. ^ Giovannoni Lab http://giovannonilab.science.oregonstate.edu/
11. ^ Giovannoni Stephen J.; Stingl Ulrich (2005). "Molecular diversity and ecology of microbial plankton". Nature 437 (7057): 343–348.  
12. ^ Carini, Paul; et al. (2012). "Nutrient requirements for growth of the extreme oligotroph '"Candidatus" Pelagibacter ubique’ HTCC1062 on a defined medium". ISME.  
13. ^ "Pelagibacter ubique genome". NCBI. Retrieved 27 November 2012. 
14. ^ Meyer MM, Ames TD, Smith DP, et al. (2009). "'"Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique. BMC Genomics 10: 268.  
15. ^ Poiata E; Meyer MM; Ames TD; Breaker RR (November 2009). "A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria". RNA 15 (11): 2046–56.  
16. ^ H. James Tripp; Michael S. Schwalbach; Michelle M. Meyer; Joshua B. Kitner; et al. (January 2009). "Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11". Environmental Microbiology 11 (1): 230–8.  
17. ^ Steindler Laura; Schwalbach Michael S.; Smith Daniel P.; Chan Francis; et al. "Energy Starved Candidatus Pelagibacter Ubique Substitutes Light-Mediated ATP Production for Endogenous Carbon Respiration". PLOS ONE 6 (5): 9999.  
18. ^ Gregory R. Crane. "pelagus entry in Perseus Digital Library". Perseus Digital Library Project. Tufts University. Retrieved 22 May 2011. 
19. ^ Lapage, S.; Sneath, P.; Lessel, E.; Skerman, V.; Seeliger, H.; Clark, W. (1992). International Code of Nomenclature of Bacteria: Bacteriological Code, 1990 Revision. Washington, D.C.: ASM Press.  
20. ^ http://www.bacterio.cict.fr/minimalstandards.html
21. ^ Murray, R. G. E.; Schleifer, K. H. (1994). "Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes". Int. J. Syst. Bacteriol 44 (1): 174–176.  
22. ^ JUDICIAL COMMISSION OF THE INTERNATIONAL COMMITTEE ON SYSTEMATIC BACTERIOLOGY: Minutes of the meetings, 2 and 6 July 1994, Prague, Czech Republic" Int. J. Syst. Bacteriol 1995; 45, 195-196.
23. ^ Euzéby J.P. (2010). "Introduction". List of Prokaryotic names with Standing in Nomenclature. Retrieved 2010-12-16. 
24. ^ Sneath, P.H.A (1992). Lapage S.P.; Sneath, P.H.A.; Lessel, E.F.; Skerman, V.B.D.; Seeliger, H.P.R.; Clark, W.A., ed. International Code of Nomenclature of Bacteria. Washington, D.C.: American Society for Microbiology.  
25. ^ Thrash, J. C.; Boyd, A.; Huggett, M. J.; Grote, J.; Carini, P.; Yoder, R. J.; Robbertse, B.; Spatafora, J. W.; Rappé, M. S.; Giovannoni, S. J. (2011). "Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade". Scientific Reports 1: 13.  
26. ^ "Flea market: A newly discovered virus may be the most abundant organism on the planet".  

External links

• MicrobeWiki entry
• BBC News: Ocean bug has 'smallest genome'

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Categories

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Bacteriophage

HTTC1062 is the type strain of the species Pelagibacter ubique, which in turn is the type species of the genus Pelagibacter,^[1] which in turn is the type genus of the SAR11 clade or family "Pelagibacteraceae".^[25]

The term "Candidatus" is used for proposed species for which the lack of information (cf.^[20]) prevents it from being a validated species according to the bacteriological code,^[21][22] such as deposition in two public cell repositories or lack of FAME analysis^[23][24] whereas "Cadidatus Pelagibacter ubique" is not in ATCC [4] and DSMZ [5], nor has analysis of lipids and quinones been conducted.

The name of the genus (Pelagibacter) stems from the Latin masculine noun pelagus ("sea") combined with the suffix -bacter (rod, bacterium), to mean "bacterium of the sea". The connecting vowel is an "i" and not an "o", as the first term is the Latin "pelagus" and not the Greek original πέλαγος (pelagos) (the word pelagus is a Greek word used in Latin poetry, it is a 2nd declension noun with a Greek-like irregular nominative plural pelagē and not pelagi^[18]). The name of the specific epithet (ubique) is a Latin adverb meaning "everywhere"; it should be noted species with the status Candidatus are not validly published so do not have to be grammatically correct, such as having specific epithets having to be adjectives or nouns in apposition in the nominative case or genitive nouns according to rule 12c of the IBCN.^[19]

Name

It is found to have proteorhodopsin genes, which help power light-mediated proton pumps. Subtle differences arise in the expression of its codon sequences when it is subjected to either light or dark treatments. More genes for oxidative phosphorylation are expressed when it is subject to darkness.^[17]

SAM-V riboswitch, and other cis-regulatory elements like the rpsB motif.^[14][15] Another example of an important ncRNA in P. ubique and other SAR11 clade members is a conserved, glycine-activated riboswitch on malate synthase, putatively leading to "functional auxotrophy" for glycine or glycine precursors in order to achieve optimal growth.^[16]

[6]